Goal: Do an MDS plot using Irene’s SNPs to look for relatedness among plants

Snp calling with freebayes

First, need to call SNPs using all BAM files at once:

working in directory 2019/IreneSnps on whitney

first, sort bams

for f in SNPanalysis/*LT*rmdup.bam
    do 
       newname=`basename $f .bam`_sort.bam
       samtools sort -o $newname --reference SNPanalysis/Pinsaporeference1 $f 
    done

next, assign read groups to bams

input=""

for f in `ls *sort.bam`
   do
      rg=`basename $f _rmdup_sort.bam`
      input="$input -b $f -r $rg -s $rg"
  done

echo $input

bamaddrg $input > LT_rmdup_sort_combined.bam

samtools index LT_rmdup_sort_combined.bam
freebayes -f SNPanalysis/Pinsaporeference1 --no-indels --no-mnps --no-complex LT_rmdup_sort_combined.bam > LT.vcf &

try parallel

ulimit -n 4000
/usr/local/stow/freebayes/scripts/fasta_generate_regions.py Pinsaporeference1.fai 100000 > regions
./freebayes-parallel regions 8 -f Pinsaporeference1 --no-indels --no-mnps --no-complex LT_rmdup_sort_combined.bam > LT.vcf 

(note: I edited the freebayes-parallel script so that it would work…)

Freeybayes parallel takes about 12 hours

scp whitney.plb.ucdavis.edu:2019/IreneSnps/LT.vcf.gz ../input/

now analyze vcf in R

library(tidyverse)
── Attaching packages ────────────────────────────────────────────────────────────────── tidyverse 1.2.1 ──
✔ ggplot2 3.0.0     ✔ purrr   0.2.5
✔ tibble  1.4.2     ✔ dplyr   0.7.6
✔ tidyr   0.8.1     ✔ stringr 1.3.1
✔ readr   1.1.1     ✔ forcats 0.3.0
── Conflicts ───────────────────────────────────────────────────────────────────── tidyverse_conflicts() ──
✖ dplyr::filter() masks stats::filter()
✖ dplyr::lag()    masks stats::lag()
library(ggrepel)

get the vcf header

vcf.header <- system("zgrep '#C' ../input/LT.vcf.gz",intern = TRUE) 
vcf.header
[1] "#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\t38LTR\t42LTR\t42LTRR\t43LTR\t43LTRR\t49LTWR\t49LTWRR\t95LTWR\t95LTWRR\t99LTWR"
vcf.header <- vcf.header %>% 
  str_replace("#","") %>% #get rid of the pound sign
  str_split(pattern = "\t") %>% #split on the tabs
  magrittr::extract2(1)
vcf.header
 [1] "CHROM"   "POS"     "ID"      "REF"     "ALT"     "QUAL"    "FILTER"  "INFO"    "FORMAT"  "38LTR"  
[11] "42LTR"   "42LTRR"  "43LTR"   "43LTRR"  "49LTWR"  "49LTWRR" "95LTWR"  "95LTWRR" "99LTWR" 

get the data

snps <- read_tsv("../input/LT.vcf.gz", na = c("","NA","."),comment="#",col_names = vcf.header) %>%
  select(-ID, -FILTER) # these are empty columns
Parsed with column specification:
cols(
  CHROM = col_character(),
  POS = col_integer(),
  ID = col_character(),
  REF = col_character(),
  ALT = col_character(),
  QUAL = col_double(),
  FILTER = col_character(),
  INFO = col_character(),
  FORMAT = col_character(),
  `38LTR` = col_character(),
  `42LTR` = col_character(),
  `42LTRR` = col_character(),
  `43LTR` = col_character(),
  `43LTRR` = col_character(),
  `49LTWR` = col_character(),
  `49LTWRR` = col_character(),
  `95LTWR` = col_character(),
  `95LTWRR` = col_character(),
  `99LTWR` = col_character()
)

|==============                                                                             |  16%   64 MB
|===============                                                                            |  16%   65 MB
|===============                                                                            |  16%   65 MB
|===============                                                                            |  16%   66 MB
|===============                                                                            |  16%   66 MB
|===============                                                                            |  16%   66 MB
|===============                                                                            |  16%   67 MB
|===============                                                                            |  16%   67 MB
|===============                                                                            |  17%   68 MB
|===============                                                                            |  17%   68 MB
|===============                                                                            |  17%   68 MB
|===============                                                                            |  17%   69 MB
|================                                                                           |  17%   69 MB
|================                                                                           |  17%   69 MB
|================                                                                           |  17%   70 MB
|================                                                                           |  17%   70 MB
|================                                                                           |  17%   71 MB
|================                                                                           |  17%   71 MB
|================                                                                           |  18%   71 MB
|================                                                                           |  18%   72 MB
|================                                                                           |  18%   72 MB
|================                                                                           |  18%   73 MB
|================                                                                           |  18%   73 MB
|=================                                                                          |  18%   73 MB
|=================                                                                          |  18%   74 MB
|=================                                                                          |  18%   74 MB
|=================                                                                          |  18%   74 MB
|=================                                                                          |  18%   75 MB
|=================                                                                          |  18%   75 MB
|=================                                                                          |  19%   76 MB
|=================                                                                          |  19%   76 MB
|=================                                                                          |  19%   76 MB
|=================                                                                          |  19%   77 MB
|=================                                                                          |  19%   77 MB
|==================                                                                         |  19%   78 MB
|==================                                                                         |  19%   78 MB
|==================                                                                         |  19%   78 MB
|==================                                                                         |  19%   79 MB
|==================                                                                         |  19%   79 MB
|==================                                                                         |  20%   79 MB
|==================                                                                         |  20%   80 MB
|==================                                                                         |  20%   80 MB
|==================                                                                         |  20%   81 MB
|==================                                                                         |  20%   81 MB
|==================                                                                         |  20%   81 MB
|==================                                                                         |  20%   82 MB
|===================                                                                        |  20%   82 MB
|===================                                                                        |  20%   83 MB
|===================                                                                        |  20%   83 MB
|===================                                                                        |  21%   83 MB
|===================                                                                        |  21%   84 MB
|===================                                                                        |  21%   84 MB
|===================                                                                        |  21%   84 MB
|===================                                                                        |  21%   85 MB
|===================                                                                        |  21%   85 MB
|===================                                                                        |  21%   86 MB
|===================                                                                        |  21%   86 MB
|====================                                                                       |  21%   86 MB
|====================                                                                       |  21%   87 MB
|====================                                                                       |  21%   87 MB
|====================                                                                       |  22%   87 MB
|====================                                                                       |  22%   88 MB
|====================                                                                       |  22%   88 MB
|====================                                                                       |  22%   89 MB
|====================                                                                       |  22%   89 MB
|====================                                                                       |  22%   89 MB
|====================                                                                       |  22%   90 MB
|====================                                                                       |  22%   90 MB
|====================                                                                       |  22%   91 MB
|=====================                                                                      |  22%   91 MB
|=====================                                                                      |  23%   91 MB
|=====================                                                                      |  23%   92 MB
|=====================                                                                      |  23%   92 MB
|=====================                                                                      |  23%   92 MB
|=====================                                                                      |  23%   93 MB
|=====================                                                                      |  23%   93 MB
|=====================                                                                      |  23%   94 MB
|=====================                                                                      |  23%   94 MB
|=====================                                                                      |  23%   94 MB
|=====================                                                                      |  23%   95 MB
|======================                                                                     |  23%   95 MB
|======================                                                                     |  24%   95 MB
|======================                                                                     |  24%   96 MB
|======================                                                                     |  24%   96 MB
|======================                                                                     |  24%   97 MB
|======================                                                                     |  24%   97 MB
|======================                                                                     |  24%   97 MB
|======================                                                                     |  24%   98 MB
|======================                                                                     |  24%   98 MB
|======================                                                                     |  24%   99 MB
|======================                                                                     |  24%   99 MB
|=======================                                                                    |  25%   99 MB
|=======================                                                                    |  25%  100 MB
|=======================                                                                    |  25%  100 MB
|=======================                                                                    |  25%  100 MB
|=======================                                                                    |  25%  101 MB
|=======================                                                                    |  25%  101 MB
|=======================                                                                    |  25%  102 MB
|=======================                                                                    |  25%  102 MB
|=======================                                                                    |  25%  102 MB
|=======================                                                                    |  25%  103 MB
|=======================                                                                    |  25%  103 MB
|=======================                                                                    |  26%  104 MB
|========================                                                                   |  26%  104 MB
|========================                                                                   |  26%  104 MB
|========================                                                                   |  26%  105 MB
|========================                                                                   |  26%  105 MB
|========================                                                                   |  26%  105 MB
|========================                                                                   |  26%  106 MB
|========================                                                                   |  26%  106 MB
|========================                                                                   |  26%  107 MB
|========================                                                                   |  26%  107 MB
|========================                                                                   |  27%  107 MB
|========================                                                                   |  27%  108 MB
|=========================                                                                  |  27%  108 MB
|=========================                                                                  |  27%  109 MB
|=========================                                                                  |  27%  109 MB
|=========================                                                                  |  27%  109 MB
|=========================                                                                  |  27%  110 MB
|=========================                                                                  |  27%  110 MB
|=========================                                                                  |  27%  110 MB
|=========================                                                                  |  27%  111 MB
|=========================                                                                  |  27%  111 MB
|=========================                                                                  |  28%  112 MB
|=========================                                                                  |  28%  112 MB
|==========================                                                                 |  28%  112 MB
|==========================                                                                 |  28%  113 MB
|==========================                                                                 |  28%  113 MB
|==========================                                                                 |  28%  114 MB
|==========================                                                                 |  28%  114 MB
|==========================                                                                 |  28%  114 MB
|==========================                                                                 |  28%  115 MB
|==========================                                                                 |  28%  115 MB
|==========================                                                                 |  29%  116 MB
|==========================                                                                 |  29%  116 MB
|==========================                                                                 |  29%  116 MB
|===========================                                                                |  29%  117 MB
|===========================                                                                |  29%  117 MB
|===========================                                                                |  29%  117 MB
|===========================                                                                |  29%  118 MB
|===========================                                                                |  29%  118 MB
|===========================                                                                |  29%  119 MB
|===========================                                                                |  29%  119 MB
|===========================                                                                |  30%  119 MB
|===========================                                                                |  30%  120 MB
|===========================                                                                |  30%  120 MB
|===========================                                                                |  30%  121 MB
|===========================                                                                |  30%  121 MB
|============================                                                               |  30%  121 MB
|============================                                                               |  30%  122 MB
|============================                                                               |  30%  122 MB
|============================                                                               |  30%  122 MB
|============================                                                               |  30%  123 MB
|============================                                                               |  31%  123 MB
|============================                                                               |  31%  124 MB
|============================                                                               |  31%  124 MB
|============================                                                               |  31%  124 MB
|============================                                                               |  31%  125 MB
|============================                                                               |  31%  125 MB
|=============================                                                              |  31%  126 MB
|=============================                                                              |  31%  126 MB
|=============================                                                              |  31%  126 MB
|=============================                                                              |  31%  127 MB
|=============================                                                              |  31%  127 MB
|=============================                                                              |  32%  128 MB
|=============================                                                              |  32%  128 MB
|=============================                                                              |  32%  128 MB
|=============================                                                              |  32%  129 MB
|=============================                                                              |  32%  129 MB
|=============================                                                              |  32%  129 MB
|==============================                                                             |  32%  130 MB
|==============================                                                             |  32%  130 MB
|==============================                                                             |  32%  131 MB
|==============================                                                             |  32%  131 MB
|==============================                                                             |  33%  131 MB
|==============================                                                             |  33%  132 MB
|==============================                                                             |  33%  132 MB
|==============================                                                             |  33%  133 MB
|==============================                                                             |  33%  133 MB
|==============================                                                             |  33%  133 MB
|==============================                                                             |  33%  134 MB
|===============================                                                            |  33%  134 MB
|===============================                                                            |  33%  135 MB
|===============================                                                            |  33%  135 MB
|===============================                                                            |  34%  135 MB
|===============================                                                            |  34%  136 MB
|===============================                                                            |  34%  136 MB
|===============================                                                            |  34%  137 MB
|===============================                                                            |  34%  137 MB
|===============================                                                            |  34%  137 MB
|===============================                                                            |  34%  138 MB
|===============================                                                            |  34%  138 MB
|================================                                                           |  34%  139 MB
|================================                                                           |  34%  139 MB
|================================                                                           |  35%  139 MB
|================================                                                           |  35%  140 MB
|================================                                                           |  35%  140 MB
|================================                                                           |  35%  141 MB
|================================                                                           |  35%  141 MB
|================================                                                           |  35%  141 MB
|================================                                                           |  35%  142 MB
|================================                                                           |  35%  142 MB
|================================                                                           |  35%  142 MB
|=================================                                                          |  35%  143 MB
|=================================                                                          |  36%  143 MB
|=================================                                                          |  36%  144 MB
|=================================                                                          |  36%  144 MB
|=================================                                                          |  36%  144 MB
|=================================                                                          |  36%  145 MB
|=================================                                                          |  36%  145 MB
|=================================                                                          |  36%  146 MB
|=================================                                                          |  36%  146 MB
|=================================                                                          |  36%  146 MB
|=================================                                                          |  36%  147 MB
|==================================                                                         |  37%  147 MB
|==================================                                                         |  37%  148 MB
|==================================                                                         |  37%  148 MB
|==================================                                                         |  37%  148 MB
|==================================                                                         |  37%  149 MB
|==================================                                                         |  37%  149 MB
|==================================                                                         |  37%  150 MB
|==================================                                                         |  37%  150 MB
|==================================                                                         |  37%  150 MB
|==================================                                                         |  37%  151 MB
|==================================                                                         |  37%  151 MB
|===================================                                                        |  38%  151 MB
|===================================                                                        |  38%  152 MB
|===================================                                                        |  38%  152 MB
|===================================                                                        |  38%  153 MB
|===================================                                                        |  38%  153 MB
|===================================                                                        |  38%  153 MB
|===================================                                                        |  38%  154 MB
|===================================                                                        |  38%  154 MB
|===================================                                                        |  38%  155 MB
|===================================                                                        |  38%  155 MB
|===================================                                                        |  39%  155 MB
|====================================                                                       |  39%  156 MB
|====================================                                                       |  39%  156 MB
|====================================                                                       |  39%  157 MB
|====================================                                                       |  39%  157 MB
|====================================                                                       |  39%  157 MB
|====================================                                                       |  39%  158 MB
|====================================                                                       |  39%  158 MB
|====================================                                                       |  39%  159 MB
|====================================                                                       |  39%  159 MB
|====================================                                                       |  40%  159 MB
|====================================                                                       |  40%  160 MB
|=====================================                                                      |  40%  160 MB
|=====================================                                                      |  40%  160 MB
|=====================================                                                      |  40%  161 MB
|=====================================                                                      |  40%  161 MB
|=====================================                                                      |  40%  162 MB
|=====================================                                                      |  40%  162 MB
|=====================================                                                      |  40%  162 MB
|=====================================                                                      |  40%  163 MB
|=====================================                                                      |  41%  163 MB
|=====================================                                                      |  41%  164 MB
|=====================================                                                      |  41%  164 MB
|======================================                                                     |  41%  164 MB
|======================================                                                     |  41%  165 MB
|======================================                                                     |  41%  165 MB
|======================================                                                     |  41%  166 MB
|======================================                                                     |  41%  166 MB
|======================================                                                     |  41%  166 MB
|======================================                                                     |  41%  167 MB
|======================================                                                     |  42%  167 MB
|======================================                                                     |  42%  168 MB
|======================================                                                     |  42%  168 MB
|======================================                                                     |  42%  168 MB
|=======================================                                                    |  42%  169 MB
|=======================================                                                    |  42%  169 MB
|=======================================                                                    |  42%  170 MB
|=======================================                                                    |  42%  170 MB
|=======================================                                                    |  42%  171 MB
|=======================================                                                    |  42%  171 MB
|=======================================                                                    |  43%  171 MB
|=======================================                                                    |  43%  172 MB
|=======================================                                                    |  43%  172 MB
|=======================================                                                    |  43%  173 MB
|========================================                                                   |  43%  173 MB
|========================================                                                   |  43%  173 MB
|========================================                                                   |  43%  174 MB
|========================================                                                   |  43%  174 MB
|========================================                                                   |  43%  175 MB
|========================================                                                   |  44%  175 MB
|========================================                                                   |  44%  175 MB
|========================================                                                   |  44%  176 MB
|========================================                                                   |  44%  176 MB
|========================================                                                   |  44%  177 MB
|========================================                                                   |  44%  177 MB
|=========================================                                                  |  44%  177 MB
|=========================================                                                  |  44%  178 MB
|=========================================                                                  |  44%  178 MB
|=========================================                                                  |  44%  179 MB
|=========================================                                                  |  44%  179 MB
|=========================================                                                  |  45%  179 MB
|=========================================                                                  |  45%  180 MB
|=========================================                                                  |  45%  180 MB
|=========================================                                                  |  45%  181 MB
|=========================================                                                  |  45%  181 MB
|=========================================                                                  |  45%  181 MB
|==========================================                                                 |  45%  182 MB
|==========================================                                                 |  45%  182 MB
|==========================================                                                 |  45%  183 MB
|==========================================                                                 |  46%  183 MB
|==========================================                                                 |  46%  183 MB
|==========================================                                                 |  46%  184 MB
|==========================================                                                 |  46%  184 MB
|==========================================                                                 |  46%  185 MB
|==========================================                                                 |  46%  185 MB
|==========================================                                                 |  46%  185 MB
|==========================================                                                 |  46%  186 MB
|===========================================                                                |  46%  186 MB
|===========================================                                                |  46%  187 MB
|===========================================                                                |  46%  187 MB
|===========================================                                                |  47%  187 MB
|===========================================                                                |  47%  188 MB
|===========================================                                                |  47%  188 MB
|===========================================                                                |  47%  188 MB
|===========================================                                                |  47%  189 MB
|===========================================                                                |  47%  189 MB
|===========================================                                                |  47%  190 MB
|===========================================                                                |  47%  190 MB
|============================================                                               |  47%  190 MB
|============================================                                               |  47%  191 MB
|============================================                                               |  48%  191 MB
|============================================                                               |  48%  192 MB
|============================================                                               |  48%  192 MB
|============================================                                               |  48%  193 MB
|============================================                                               |  48%  193 MB
|============================================                                               |  48%  193 MB
|============================================                                               |  48%  194 MB
|============================================                                               |  48%  194 MB
|============================================                                               |  48%  194 MB
|=============================================                                              |  48%  195 MB
|=============================================                                              |  49%  195 MB
|=============================================                                              |  49%  196 MB
|=============================================                                              |  49%  196 MB
|=============================================                                              |  49%  196 MB
|=============================================                                              |  49%  197 MB
|=============================================                                              |  49%  197 MB
|=============================================                                              |  49%  198 MB
|=============================================                                              |  49%  198 MB
|=============================================                                              |  49%  199 MB
|=============================================                                              |  49%  199 MB
|==============================================                                             |  50%  199 MB
|==============================================                                             |  50%  200 MB
|==============================================                                             |  50%  200 MB
|==============================================                                             |  50%  201 MB
|==============================================                                             |  50%  201 MB
|==============================================                                             |  50%  201 MB
|==============================================                                             |  50%  202 MB
|==============================================                                             |  50%  202 MB
|==============================================                                             |  50%  203 MB
|==============================================                                             |  50%  203 MB
|==============================================                                             |  51%  203 MB
|===============================================                                            |  51%  204 MB
|===============================================                                            |  51%  204 MB
|===============================================                                            |  51%  204 MB
|===============================================                                            |  51%  205 MB
|===============================================                                            |  51%  205 MB
|===============================================                                            |  51%  206 MB
|===============================================                                            |  51%  206 MB
|===============================================                                            |  51%  206 MB
|===============================================                                            |  51%  207 MB
|===============================================                                            |  52%  207 MB
|===============================================                                            |  52%  208 MB
|================================================                                           |  52%  208 MB
|================================================                                           |  52%  208 MB
|================================================                                           |  52%  209 MB
|================================================                                           |  52%  209 MB
|================================================                                           |  52%  210 MB
|================================================                                           |  52%  210 MB
|================================================                                           |  52%  210 MB
|================================================                                           |  52%  211 MB
|================================================                                           |  53%  211 MB
|================================================                                           |  53%  212 MB
|================================================                                           |  53%  212 MB
|=================================================                                          |  53%  212 MB
|=================================================                                          |  53%  213 MB
|=================================================                                          |  53%  213 MB
|=================================================                                          |  53%  213 MB
|=================================================                                          |  53%  214 MB
|=================================================                                          |  53%  214 MB
|=================================================                                          |  53%  215 MB
|=================================================                                          |  54%  215 MB
|=================================================                                          |  54%  216 MB
|=================================================                                          |  54%  216 MB
|=================================================                                          |  54%  216 MB
|==================================================                                         |  54%  217 MB
|==================================================                                         |  54%  217 MB
|==================================================                                         |  54%  217 MB
|==================================================                                         |  54%  218 MB
|==================================================                                         |  54%  218 MB
|==================================================                                         |  54%  219 MB
|==================================================                                         |  55%  219 MB
|==================================================                                         |  55%  219 MB
|==================================================                                         |  55%  220 MB
|==================================================                                         |  55%  220 MB
|==================================================                                         |  55%  221 MB
|===================================================                                        |  55%  221 MB
|===================================================                                        |  55%  221 MB
|===================================================                                        |  55%  222 MB
|===================================================                                        |  55%  222 MB
|===================================================                                        |  55%  223 MB
|===================================================                                        |  55%  223 MB
|===================================================                                        |  56%  223 MB
|===================================================                                        |  56%  224 MB
|===================================================                                        |  56%  224 MB
|===================================================                                        |  56%  224 MB
|===================================================                                        |  56%  225 MB
|====================================================                                       |  56%  225 MB
|====================================================                                       |  56%  226 MB
|====================================================                                       |  56%  226 MB
|====================================================                                       |  56%  226 MB
|====================================================                                       |  56%  227 MB
|====================================================                                       |  57%  227 MB
|====================================================                                       |  57%  228 MB
|====================================================                                       |  57%  228 MB
|====================================================                                       |  57%  228 MB
|====================================================                                       |  57%  229 MB
|====================================================                                       |  57%  229 MB
|=====================================================                                      |  57%  230 MB
|=====================================================                                      |  57%  230 MB
|=====================================================                                      |  57%  230 MB
|=====================================================                                      |  57%  231 MB
|=====================================================                                      |  58%  231 MB
|=====================================================                                      |  58%  232 MB
|=====================================================                                      |  58%  232 MB
|=====================================================                                      |  58%  232 MB
|=====================================================                                      |  58%  233 MB
|=====================================================                                      |  58%  233 MB
|=====================================================                                      |  58%  233 MB
|======================================================                                     |  58%  234 MB
|======================================================                                     |  58%  234 MB
|======================================================                                     |  58%  235 MB
|======================================================                                     |  59%  235 MB
|======================================================                                     |  59%  235 MB
|======================================================                                     |  59%  236 MB
|======================================================                                     |  59%  236 MB
|======================================================                                     |  59%  237 MB
|======================================================                                     |  59%  237 MB
|======================================================                                     |  59%  237 MB
|======================================================                                     |  59%  238 MB
|=======================================================                                    |  59%  238 MB
|=======================================================                                    |  59%  238 MB
|=======================================================                                    |  59%  239 MB
|=======================================================                                    |  60%  239 MB
|=======================================================                                    |  60%  240 MB
|=======================================================                                    |  60%  240 MB
|=======================================================                                    |  60%  240 MB
|=======================================================                                    |  60%  241 MB
|=======================================================                                    |  60%  241 MB
|=======================================================                                    |  60%  242 MB
|=======================================================                                    |  60%  242 MB
|=======================================================                                    |  60%  242 MB
|========================================================                                   |  60%  243 MB
|========================================================                                   |  61%  243 MB
|========================================================                                   |  61%  244 MB
|========================================================                                   |  61%  244 MB
|========================================================                                   |  61%  244 MB
|========================================================                                   |  61%  245 MB
|========================================================                                   |  61%  245 MB
|========================================================                                   |  61%  246 MB
|========================================================                                   |  61%  246 MB
|========================================================                                   |  61%  246 MB
|=========================================================                                  |  61%  247 MB
|=========================================================                                  |  62%  247 MB
|=========================================================                                  |  62%  248 MB
|=========================================================                                  |  62%  248 MB
|=========================================================                                  |  62%  248 MB
|=========================================================                                  |  62%  249 MB
|=========================================================                                  |  62%  249 MB
|=========================================================                                  |  62%  249 MB
|=========================================================                                  |  62%  250 MB
|=========================================================                                  |  62%  250 MB
|=========================================================                                  |  62%  251 MB
|=========================================================                                  |  63%  251 MB
|==========================================================                                 |  63%  251 MB
|==========================================================                                 |  63%  252 MB
|==========================================================                                 |  63%  252 MB
|==========================================================                                 |  63%  253 MB
|==========================================================                                 |  63%  253 MB
|==========================================================                                 |  63%  253 MB
|==========================================================                                 |  63%  254 MB
|==========================================================                                 |  63%  254 MB
|==========================================================                                 |  63%  255 MB
|==========================================================                                 |  64%  255 MB
|==========================================================                                 |  64%  255 MB
|===========================================================                                |  64%  256 MB
|===========================================================                                |  64%  256 MB
|===========================================================                                |  64%  256 MB
|===========================================================                                |  64%  257 MB
|===========================================================                                |  64%  257 MB
|===========================================================                                |  64%  258 MB
|===========================================================                                |  64%  258 MB
|===========================================================                                |  64%  258 MB
|===========================================================                                |  64%  259 MB
|===========================================================                                |  65%  259 MB
|===========================================================                                |  65%  260 MB
|============================================================                               |  65%  260 MB
|============================================================                               |  65%  260 MB
|============================================================                               |  65%  261 MB
|============================================================                               |  65%  261 MB
|============================================================                               |  65%  262 MB
|============================================================                               |  65%  262 MB
|============================================================                               |  65%  262 MB
|============================================================                               |  65%  263 MB
|============================================================                               |  66%  263 MB
|============================================================                               |  66%  264 MB
|============================================================                               |  66%  264 MB
|=============================================================                              |  66%  264 MB
|=============================================================                              |  66%  265 MB
|=============================================================                              |  66%  265 MB
|=============================================================                              |  66%  265 MB
|=============================================================                              |  66%  266 MB
|=============================================================                              |  66%  266 MB
|=============================================================                              |  66%  267 MB
|=============================================================                              |  67%  267 MB
|=============================================================                              |  67%  267 MB
|=============================================================                              |  67%  268 MB
|=============================================================                              |  67%  268 MB
|==============================================================                             |  67%  269 MB
|==============================================================                             |  67%  269 MB
|==============================================================                             |  67%  269 MB
|==============================================================                             |  67%  270 MB
|==============================================================                             |  67%  270 MB
|==============================================================                             |  67%  271 MB
|==============================================================                             |  68%  271 MB
|==============================================================                             |  68%  271 MB
|==============================================================                             |  68%  272 MB
|==============================================================                             |  68%  272 MB
|==============================================================                             |  68%  273 MB
|===============================================================                            |  68%  273 MB
|===============================================================                            |  68%  273 MB
|===============================================================                            |  68%  274 MB
|===============================================================                            |  68%  274 MB
|===============================================================                            |  68%  274 MB
|===============================================================                            |  69%  275 MB
|===============================================================                            |  69%  275 MB
|===============================================================                            |  69%  276 MB
|===============================================================                            |  69%  276 MB
|===============================================================                            |  69%  277 MB
|===============================================================                            |  69%  277 MB
|================================================================                           |  69%  277 MB
|================================================================                           |  69%  278 MB
|================================================================                           |  69%  278 MB
|================================================================                           |  69%  279 MB
|================================================================                           |  70%  279 MB
|================================================================                           |  70%  279 MB
|================================================================                           |  70%  280 MB
|================================================================                           |  70%  280 MB
|================================================================                           |  70%  280 MB
|================================================================                           |  70%  281 MB
|================================================================                           |  70%  281 MB
|=================================================================                          |  70%  282 MB
|=================================================================                          |  70%  282 MB
|=================================================================                          |  70%  282 MB
|=================================================================                          |  71%  283 MB
|=================================================================                          |  71%  283 MB
|=================================================================                          |  71%  284 MB
|=================================================================                          |  71%  284 MB
|=================================================================                          |  71%  284 MB
|=================================================================                          |  71%  285 MB
|=================================================================                          |  71%  285 MB
|=================================================================                          |  71%  285 MB
|==================================================================                         |  71%  286 MB
|==================================================================                         |  71%  286 MB
|==================================================================                         |  71%  287 MB
|==================================================================                         |  72%  287 MB
|==================================================================                         |  72%  287 MB
|==================================================================                         |  72%  288 MB
|==================================================================                         |  72%  288 MB
|==================================================================                         |  72%  289 MB
|==================================================================                         |  72%  289 MB
|==================================================================                         |  72%  289 MB
|==================================================================                         |  72%  290 MB
|===================================================================                        |  72%  290 MB
|===================================================================                        |  72%  290 MB
|===================================================================                        |  73%  291 MB
|===================================================================                        |  73%  291 MB
|===================================================================                        |  73%  292 MB
|===================================================================                        |  73%  292 MB
|===================================================================                        |  73%  292 MB
|===================================================================                        |  73%  293 MB
|===================================================================                        |  73%  293 MB
|===================================================================                        |  73%  294 MB
|===================================================================                        |  73%  294 MB
|====================================================================                       |  73%  294 MB
|====================================================================                       |  74%  295 MB
|====================================================================                       |  74%  295 MB
|====================================================================                       |  74%  296 MB
|====================================================================                       |  74%  296 MB
|====================================================================                       |  74%  296 MB
|====================================================================                       |  74%  297 MB
|====================================================================                       |  74%  297 MB
|====================================================================                       |  74%  298 MB
|====================================================================                       |  74%  298 MB
|====================================================================                       |  74%  298 MB
|====================================================================                       |  74%  299 MB
|=====================================================================                      |  75%  299 MB
|=====================================================================                      |  75%  299 MB
|=====================================================================                      |  75%  300 MB
|=====================================================================                      |  75%  300 MB
|=====================================================================                      |  75%  301 MB
|=====================================================================                      |  75%  301 MB
|=====================================================================                      |  75%  301 MB
|=====================================================================                      |  75%  302 MB
|=====================================================================                      |  75%  302 MB
|=====================================================================                      |  75%  303 MB
|=====================================================================                      |  76%  303 MB
|======================================================================                     |  76%  303 MB
|======================================================================                     |  76%  304 MB
|======================================================================                     |  76%  304 MB
|======================================================================                     |  76%  304 MB
|======================================================================                     |  76%  305 MB
|======================================================================                     |  76%  305 MB
|======================================================================                     |  76%  306 MB
|======================================================================                     |  76%  306 MB
|======================================================================                     |  76%  306 MB
|======================================================================                     |  77%  307 MB
|======================================================================                     |  77%  307 MB
|=======================================================================                    |  77%  308 MB
|=======================================================================                    |  77%  308 MB
|=======================================================================                    |  77%  308 MB
|=======================================================================                    |  77%  309 MB
|=======================================================================                    |  77%  309 MB
|=======================================================================                    |  77%  310 MB
|=======================================================================                    |  77%  310 MB
|=======================================================================                    |  77%  310 MB
|=======================================================================                    |  78%  311 MB
|=======================================================================                    |  78%  311 MB
|=======================================================================                    |  78%  312 MB
|========================================================================                   |  78%  312 MB
|========================================================================                   |  78%  312 MB
|========================================================================                   |  78%  313 MB
|========================================================================                   |  78%  313 MB
|========================================================================                   |  78%  313 MB
|========================================================================                   |  78%  314 MB
|========================================================================                   |  78%  314 MB
|========================================================================                   |  78%  315 MB
|========================================================================                   |  79%  315 MB
|========================================================================                   |  79%  315 MB
|========================================================================                   |  79%  316 MB
|=========================================================================                  |  79%  316 MB
|=========================================================================                  |  79%  317 MB
|=========================================================================                  |  79%  317 MB
|=========================================================================                  |  79%  317 MB
|=========================================================================                  |  79%  318 MB
|=========================================================================                  |  79%  318 MB
|=========================================================================                  |  79%  319 MB
|=========================================================================                  |  80%  319 MB
|=========================================================================                  |  80%  319 MB
|=========================================================================                  |  80%  320 MB
|=========================================================================                  |  80%  320 MB
|==========================================================================                 |  80%  320 MB
|==========================================================================                 |  80%  321 MB
|==========================================================================                 |  80%  321 MB
|==========================================================================                 |  80%  322 MB
|==========================================================================                 |  80%  322 MB
|==========================================================================                 |  80%  322 MB
|==========================================================================                 |  81%  323 MB
|==========================================================================                 |  81%  323 MB
|==========================================================================                 |  81%  324 MB
|==========================================================================                 |  81%  324 MB
|==========================================================================                 |  81%  324 MB
|===========================================================================                |  81%  325 MB
|===========================================================================                |  81%  325 MB
|===========================================================================                |  81%  326 MB
|===========================================================================                |  81%  326 MB
|===========================================================================                |  81%  326 MB
|===========================================================================                |  82%  327 MB
|===========================================================================                |  82%  327 MB
|===========================================================================                |  82%  328 MB
|===========================================================================                |  82%  328 MB
|===========================================================================                |  82%  328 MB
|===========================================================================                |  82%  329 MB
|============================================================================               |  82%  329 MB
|============================================================================               |  82%  330 MB
|============================================================================               |  82%  330 MB
|============================================================================               |  82%  330 MB
|============================================================================               |  83%  331 MB
|============================================================================               |  83%  331 MB
|============================================================================               |  83%  332 MB
|============================================================================               |  83%  332 MB
|============================================================================               |  83%  332 MB
|============================================================================               |  83%  333 MB
|============================================================================               |  83%  333 MB
|=============================================================================              |  83%  333 MB
|=============================================================================              |  83%  334 MB
|=============================================================================              |  83%  334 MB
|=============================================================================              |  83%  335 MB
|=============================================================================              |  84%  335 MB
|=============================================================================              |  84%  335 MB
|=============================================================================              |  84%  336 MB
|=============================================================================              |  84%  336 MB
|=============================================================================              |  84%  337 MB
|=============================================================================              |  84%  337 MB
|=============================================================================              |  84%  337 MB
|=============================================================================              |  84%  338 MB
|==============================================================================             |  84%  338 MB
|==============================================================================             |  84%  339 MB
|==============================================================================             |  85%  339 MB
|==============================================================================             |  85%  339 MB
|==============================================================================             |  85%  340 MB
|==============================================================================             |  85%  340 MB
|==============================================================================             |  85%  341 MB
|==============================================================================             |  85%  341 MB
|==============================================================================             |  85%  341 MB
|==============================================================================             |  85%  342 MB
|===============================================================================            |  85%  342 MB
|===============================================================================            |  85%  343 MB
|===============================================================================            |  86%  343 MB
|===============================================================================            |  86%  343 MB
|===============================================================================            |  86%  344 MB
|===============================================================================            |  86%  344 MB
|===============================================================================            |  86%  345 MB
|===============================================================================            |  86%  345 MB
|===============================================================================            |  86%  345 MB
|===============================================================================            |  86%  346 MB
|===============================================================================            |  86%  346 MB
|================================================================================           |  86%  346 MB
|================================================================================           |  87%  347 MB
|================================================================================           |  87%  347 MB
|================================================================================           |  87%  348 MB
|================================================================================           |  87%  348 MB
|================================================================================           |  87%  348 MB
|================================================================================           |  87%  349 MB
|================================================================================           |  87%  349 MB
|================================================================================           |  87%  349 MB
|================================================================================           |  87%  350 MB
|================================================================================           |  87%  350 MB
|================================================================================           |  88%  351 MB
|=================================================================================          |  88%  351 MB
|=================================================================================          |  88%  351 MB
|=================================================================================          |  88%  352 MB
|=================================================================================          |  88%  352 MB
|=================================================================================          |  88%  352 MB
|=================================================================================          |  88%  353 MB
|=================================================================================          |  88%  353 MB
|=================================================================================          |  88%  354 MB
|=================================================================================          |  88%  354 MB
|=================================================================================          |  88%  354 MB
|=================================================================================          |  89%  355 MB
|=================================================================================          |  89%  355 MB
|==================================================================================         |  89%  355 MB
|==================================================================================         |  89%  356 MB
|==================================================================================         |  89%  356 MB
|==================================================================================         |  89%  357 MB
|==================================================================================         |  89%  357 MB
|==================================================================================         |  89%  357 MB
|==================================================================================         |  89%  358 MB
|==================================================================================         |  89%  358 MB
|==================================================================================         |  89%  358 MB
|==================================================================================         |  90%  359 MB
|==================================================================================         |  90%  359 MB
|==================================================================================         |  90%  359 MB
|===================================================================================        |  90%  360 MB
|===================================================================================        |  90%  360 MB
|===================================================================================        |  90%  360 MB
|===================================================================================        |  90%  361 MB
|===================================================================================        |  90%  361 MB
|===================================================================================        |  90%  362 MB
|===================================================================================        |  90%  362 MB
|===================================================================================        |  90%  362 MB
|===================================================================================        |  91%  363 MB
|===================================================================================        |  91%  363 MB
|===================================================================================        |  91%  364 MB
|====================================================================================       |  91%  364 MB
|====================================================================================       |  91%  364 MB
|====================================================================================       |  91%  365 MB
|====================================================================================       |  91%  365 MB
|====================================================================================       |  91%  366 MB
|====================================================================================       |  91%  366 MB
|====================================================================================       |  91%  366 MB
|====================================================================================       |  92%  367 MB
|====================================================================================       |  92%  367 MB
|====================================================================================       |  92%  367 MB
|====================================================================================       |  92%  368 MB
|=====================================================================================      |  92%  368 MB
|=====================================================================================      |  92%  369 MB
|=====================================================================================      |  92%  369 MB
|=====================================================================================      |  92%  369 MB
|=====================================================================================      |  92%  370 MB
|=====================================================================================      |  92%  370 MB
|=====================================================================================      |  92%  370 MB
|=====================================================================================      |  93%  371 MB
|=====================================================================================      |  93%  371 MB
|=====================================================================================      |  93%  372 MB
|=====================================================================================      |  93%  372 MB
|=====================================================================================      |  93%  372 MB
|======================================================================================     |  93%  373 MB
|======================================================================================     |  93%  373 MB
|======================================================================================     |  93%  373 MB
|======================================================================================     |  93%  374 MB
|======================================================================================     |  93%  374 MB
|======================================================================================     |  93%  374 MB
|======================================================================================     |  94%  375 MB
|======================================================================================     |  94%  375 MB
|======================================================================================     |  94%  375 MB
|======================================================================================     |  94%  376 MB
|======================================================================================     |  94%  376 MB
|======================================================================================     |  94%  377 MB
|=======================================================================================    |  94%  377 MB
|=======================================================================================    |  94%  377 MB
|=======================================================================================    |  94%  378 MB
|=======================================================================================    |  94%  378 MB
|=======================================================================================    |  94%  378 MB
|=======================================================================================    |  95%  379 MB
|=======================================================================================    |  95%  379 MB
|=======================================================================================    |  95%  379 MB
|=======================================================================================    |  95%  380 MB
|=======================================================================================    |  95%  380 MB
|=======================================================================================    |  95%  380 MB
|=======================================================================================    |  95%  381 MB
|========================================================================================   |  95%  381 MB
|========================================================================================   |  95%  382 MB
|========================================================================================   |  95%  382 MB
|========================================================================================   |  95%  382 MB
|========================================================================================   |  95%  383 MB
|========================================================================================   |  96%  383 MB
|========================================================================================   |  96%  383 MB
|========================================================================================   |  96%  384 MB
|========================================================================================   |  96%  384 MB
|========================================================================================   |  96%  384 MB
|========================================================================================   |  96%  385 MB
|========================================================================================   |  96%  385 MB
|========================================================================================   |  96%  385 MB
|=========================================================================================  |  96%  386 MB
|=========================================================================================  |  96%  386 MB
|=========================================================================================  |  96%  386 MB
|=========================================================================================  |  97%  387 MB
|=========================================================================================  |  97%  387 MB
|=========================================================================================  |  97%  387 MB
|=========================================================================================  |  97%  388 MB
|=========================================================================================  |  97%  388 MB
|=========================================================================================  |  97%  388 MB
|=========================================================================================  |  97%  389 MB
|=========================================================================================  |  97%  389 MB
|=========================================================================================  |  97%  389 MB
|=========================================================================================  |  97%  390 MB
|========================================================================================== |  97%  390 MB
|========================================================================================== |  97%  390 MB
|========================================================================================== |  98%  391 MB
|========================================================================================== |  98%  391 MB
|========================================================================================== |  98%  391 MB
|========================================================================================== |  98%  392 MB
|========================================================================================== |  98%  392 MB
|========================================================================================== |  98%  392 MB
|========================================================================================== |  98%  393 MB
|========================================================================================== |  98%  393 MB
|========================================================================================== |  98%  393 MB
|========================================================================================== |  98%  394 MB
|========================================================================================== |  98%  394 MB
|===========================================================================================|  98%  394 MB
|===========================================================================================|  99%  395 MB
|===========================================================================================|  99%  395 MB
|===========================================================================================|  99%  395 MB
|===========================================================================================|  99%  396 MB
|===========================================================================================|  99%  396 MB
|===========================================================================================|  99%  396 MB
|===========================================================================================|  99%  397 MB
|===========================================================================================|  99%  397 MB
|===========================================================================================|  99%  397 MB
|===========================================================================================|  99%  398 MB
|===========================================================================================|  99%  398 MB
|===========================================================================================|  99%  398 MB
|============================================================================================| 100%  398 MB
snps

filter to keep snps where there is data from all samples

snps <- snps %>% 
  filter({select(., matches("[0-9]")) %>% complete.cases() })
snps
snps <- snps %>% 
  mutate(TOTAL_DEPTH= {str_extract(INFO, "DP=[0-9]*") %>% 
      str_remove("DP=") %>%
      as.numeric() }
  ) %>%
  filter(QUAL >=100,
         nchar(ALT)==1,
         TOTAL_DEPTH > quantile(TOTAL_DEPTH, 0.05),
         TOTAL_DEPTH < quantile(TOTAL_DEPTH, 0.95))
snps

unpack the information differnet samples:

samples <- colnames(snps) %>% str_subset("^[0-9]")
for (s in samples) {
snps <- snps %>%
  separate(!!s, into=paste(s,c("gt","tot.depth","allele.depth","ref.depth","ref.qual","alt.depth","alt.qual","gt.lik"),sep="_"),
           sep=":", convert = TRUE)
}
snps

For the MDS we only need the genotype info

gts <- snps %>%
  select(ends_with("_gt"))
gts

convert this to numeric

geno.numeric <- gts %>%
  lapply(factor) %>% # convert charcters to "factors", where each category is internally represented as a number
  as.data.frame() %>% # reformat
  data.matrix() %>%#  convert to numeric
  t() 
head(geno.numeric[,1:5],10)
            [,1] [,2] [,3] [,4] [,5]
X38LTR_gt      2    2    2    2    2
X42LTR_gt      2    3    2    2    2
X42LTRR_gt     2    2    2    2    1
X43LTR_gt      2    2    2    2    2
X43LTRR_gt     2    2    2    2    2
X49LTWR_gt     2    2    2    2    2
X49LTWRR_gt    3    3    3    3    1
X95LTWR_gt     2    3    3    2    2
X95LTWRR_gt    2    3    3    2    2
X99LTWR_gt     2    2    2    2    2
dim(geno.numeric)
[1]     10 134421
dim(gts)
[1] 134421     10
genDist <- as.matrix(dist(geno.numeric))
dim(genDist)
[1] 10 10
#perform the multi-dimensional scaling
geno.mds <- as.tibble(cmdscale(genDist))
geno.mds$ID <- rownames(geno.numeric) 
geno.mds <- geno.mds %>%
  mutate(ID={str_replace(ID, "W", "N") %>%
       str_replace("RR", "R2") %>%
      str_remove_all("(X|_gt)") },
    response=ifelse(str_detect(ID,"N"), "no recovery", "recovery"))
geno.mds
geno.mds %>%
  ggplot(aes(x=V1, y = V2, label=ID, color=response)) +
  geom_point() +
  geom_text_repel(show.legend=FALSE, direction="y")

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